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Magnesium in PDB 6vpl: TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp

Enzymatic activity of TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp

All present enzymatic activity of TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp:
2.7.11.1;

Protein crystallography data

The structure of TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp, PDB code: 6vpl was solved by D.C.Lim, M.B.Yaffe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.07 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.637, 85.562, 152.934, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.1

Other elements in 6vpl:

The structure of TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp (pdb code 6vpl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp, PDB code: 6vpl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6vpl

Go back to Magnesium Binding Sites List in 6vpl
Magnesium binding site 1 out of 4 in the TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:38.6
occ:1.00
 OD2 A:ASP11 2.5 21.3 1.0
OE1 B:GLU175 2.5 26.3 1.0
O B:SER7 2.5 26.4 1.0
CD B:GLU175 3.2 31.3 1.0
OE2 B:GLU175 3.3 29.8 1.0
CG A:ASP11 3.4 23.7 1.0
O B:HOH861 3.5 27.4 1.0
CD2 B:HIS176 3.5 19.3 1.0
C B:SER7 3.6 26.6 1.0
N B:SER7 3.7 27.9 1.0
NH1 B:ARG179 3.7 14.9 1.0
OD1 A:ASP11 3.7 25.4 1.0
NE2 B:HIS176 3.7 20.4 1.0
CA B:SER7 4.0 28.4 1.0
CD B:ARG179 4.1 19.3 1.0
CB B:SER7 4.2 32.4 1.0
CZ B:ARG179 4.3 21.9 1.0
CE B:MET-1 4.3 32.9 0.6
CB B:MET-1 4.3 32.8 0.6
CB B:MET-1 4.3 33.4 0.4
NE B:ARG179 4.4 18.1 1.0
CE2 B:TYR10 4.5 19.0 1.0
C B:MET-1 4.5 34.3 1.0
CG B:GLU175 4.6 29.6 1.0
N B:TYR8 4.7 22.8 1.0
OG B:SER7 4.8 27.0 1.0
CB A:ASP11 4.8 21.8 1.0
CG B:HIS176 4.9 19.3 1.0
CA B:MET-1 4.9 34.1 1.0
CB B:ARG179 4.9 13.0 1.0
O B:GLU175 5.0 16.3 1.0
CE B:MET-1 5.0 35.9 0.4

Magnesium binding site 2 out of 4 in 6vpl

Go back to Magnesium Binding Sites List in 6vpl
Magnesium binding site 2 out of 4 in the TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:56.4
occ:1.00
 O3G A:ANP602 2.9 95.8 0.8
OE1 A:GLU181 3.0 23.8 1.0
O A:HOH825 3.2 43.5 1.0
O A:HOH740 3.3 39.8 1.0
NZ A:LYS162 3.3 41.0 1.0
CD A:GLU181 3.8 24.7 1.0
O A:HOH890 3.8 38.7 1.0
CD2 A:LEU164 3.9 32.5 1.0
OE2 A:GLU181 3.9 22.0 1.0
CD1 A:LEU178 3.9 20.8 1.0
CE A:LYS162 4.3 34.7 1.0
PG A:ANP602 4.4 96.8 0.8
O A:HOH893 4.7 43.9 1.0
N3B A:ANP602 4.8 94.4 0.8
O2G A:ANP602 5.0 97.8 0.8

Magnesium binding site 3 out of 4 in 6vpl

Go back to Magnesium Binding Sites List in 6vpl
Magnesium binding site 3 out of 4 in the TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:42.6
occ:1.00
 OE1 A:GLU175 2.3 38.7 1.0
O A:SER7 2.4 38.0 1.0
OD2 B:ASP11 2.6 23.9 1.0
CD A:GLU175 3.1 37.8 1.0
OE2 A:GLU175 3.2 35.2 1.0
O A:HOH869 3.4 28.1 1.0
C A:SER7 3.5 34.8 1.0
CG B:ASP11 3.5 24.0 1.0
CD2 A:HIS176 3.5 20.6 1.0
NH1 A:ARG179 3.6 15.3 1.0
OD1 B:ASP11 3.8 26.3 1.0
NE2 A:HIS176 3.8 20.9 1.0
N A:SER7 3.9 32.5 1.0
CD A:ARG179 4.1 16.0 1.0
CA A:SER7 4.1 32.7 1.0
CB A:SER7 4.2 36.3 1.0
CZ A:ARG179 4.3 17.0 1.0
CG A:MET-1 4.4 56.1 1.0
NE A:ARG179 4.4 16.6 1.0
CE2 A:TYR10 4.4 23.4 1.0
CG A:GLU175 4.6 35.8 1.0
CE A:MET-1 4.6 60.5 1.0
N A:TYR8 4.6 21.2 1.0
OG A:SER7 4.6 31.3 1.0
CG A:HIS176 4.9 19.2 1.0
CB A:ARG179 4.9 15.5 1.0
CB B:ASP11 4.9 22.7 1.0
CA A:TYR8 4.9 19.3 1.0
C A:MET-1 4.9 42.0 1.0
O A:GLU175 5.0 18.8 1.0

Magnesium binding site 4 out of 4 in 6vpl

Go back to Magnesium Binding Sites List in 6vpl
Magnesium binding site 4 out of 4 in the TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of TPX2 Residues 7-20 Fused to Aurora A Residues 116-389 with C290 Disulfide Bonded to Compound 7-80, and in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:63.7
occ:1.00
 O2G B:ANP601 2.1 73.2 0.7
OE1 B:GLU181 2.9 28.6 1.0
NZ B:LYS162 3.1 45.4 1.0
OE2 B:GLU181 3.6 24.7 1.0
O B:HOH715 3.6 31.2 1.0
CD B:GLU181 3.6 27.6 1.0
PG B:ANP601 3.7 76.9 0.7
CE B:LYS162 3.8 43.1 1.0
CD1 B:LEU178 3.9 14.5 1.0
CD2 B:LEU164 4.2 37.0 1.0
O3G B:ANP601 4.3 68.5 0.7
N3B B:ANP601 4.3 76.8 0.7
O B:HOH889 4.4 35.6 1.0
O1G B:ANP601 4.6 80.1 0.7
CD B:LYS162 4.7 34.0 1.0
CD2 B:LEU208 5.0 22.8 1.0
O B:HOH929 5.0 44.9 1.0

Reference:

D.C.Lim, V.Joukov, T.J.Rettenmaier, A.Kumagai, W.G.Dunphy, J.A.Wells, M.B.Yaffe. Redox Priming Promotes Aurora A Activation During Mitosis. Sci.Signal. V. 13 2020.
ISSN: ESSN 1937-9145
PubMed: 32694171
DOI: 10.1126/SCISIGNAL.ABB6707
Page generated: Tue Oct 1 22:12:01 2024

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